\chapter*{Introduction}

%Many fundamental features of \brahms have been developed by following accepted standards and sometimes by merging together existing pieces of work.\footnote{This should hardly  be surprising, given that molecular dynamics is a very simple technique (requiring little more than basic Newtonian physics and a computer) which has been around for several decades now. There are in fact many codes around, together with several textbooks and countless articles. Clearly, it is much better to ``stand on the shoulders of giants'' than ``reinventing the wheel''.}  

The \brahms manual is organized in two parts. Part I is the ``proper'' manual; it describes how to run \brahms and what to do with the data generated. Part II provides background material on several topics related to the \brahms project.

\noindent \\The following paragraphs point to references which can be very useful to fully understand various aspects of the \brahms project.

\paragraph{The Art of Molecular Dynamics Simulation} This excellent book
by D.C. Rapaport~\cite{rapa} constitutes the basis of many crucial components of \brahms. There is no better introduction to \brahms than this textbook and associated
software. \brahms users are invited to study chapters 1-6, 8 and 9, and run the examples. \brahms developers should also consider chapters 17 and 18.

\paragraph{Gromacs manual} The manual of the popular Gromacs code~\cite{gmx31} contains some material which is relevant to Brahms. In particular, \brahms adopts the same
convention regarding units. This reference is also recommended as a good general introduction to practical aspects of molecular dynamics simulations.

\paragraph{Life - as a matter of fat~\cite{mouritsen}} Good book on lipid membranes, covering both modeling and experimental aspects; this is a very useful and relevant reference that touches on many aspects of the \brahms project.

\paragraph{Membrane force field} \brahms implements the coarse-grain ELBA force field, which is described in the literature.~\cite{orsi11elba}

\paragraph{Rigid-body integration} The efficiency of {\sc brahms} has been optimized through the implementation of the advanced molecular dynamics integration 
scheme invented by Dullweber et al;~\cite{dullw97a} this reference also covers some general background on rigid-body dynamics, which is a non-standard feature of 
molecular dynamics (most available codes, including for example Gromacs, Namd and Charmm, cannot simulate rigid body dynamics). See also section~\ref{sec:rigidBodies}.

